During the battle, Luke Skywalker and his Jedi team engaged Palpatine,his Dark Jedi and Imperial Guards in a fierce duel, which resulted the final death of Darth Sidious and his escorts. However, two Jedi Rayf Ysanna and Empatojayos Brand were killed while several members of the Jedi team received various injuries.

Meanwhile, a Rebel strike team lead by Lando Calrissian and Kam Solusar struck the Imperial flagship Eclipse II and succeeded in sabotaging the vessel's automated hyperdrive engines. This set the vessel on a course for the Imperial throneworld of Byss in the Deep Core where it would exit hyperspace at the precise location of the Galaxy Gun—another of the Emperor's superweapons. The resulting explosion destroyed the two massive weapons of war while the planet Byss itself was destroyed by a loose projectile.

The death of Emperor Palpatine on Onderon and the destruction of Byss and the surrounding Imperial fleet scored a heavy blow for the New Republic against the Imperial Remnant, which fragmented into several factions.

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Having returned in yet another clone, Palpatine continued his campaign against the New Republic. Armed with the deadly superweapons, the Galaxy Gun and his Eclipse-class Super Star DestroyerEclipse II, Palpatine forced many New Republic worlds to submit to Imperial rule. Despite his the growth of his Empire, Palpatine was again growing frail and weak.[4]

The resurrected Emperor also began to succumb to accelerated aging due to genetic tampering done to his clones by the treacherous Sovereign ProtectorCarnor Jax. He tried to clone other bodies so that he could resurrect himself, but Jax had succeeded in tainting even the genetic source material.[3]

Even his scientists and doctors were rendered helpless. With his body wasting away rapidly, he went to the Sith world Korriban to consult the ancient Sith Lords. Clearly stating that even they could do nothing about his degenerating body, they advised him to gaze into the Oracle stone, where he saw Anakin Solo. The Sith told him that this boy would either be his salvation or his bright doom. They told him where to find him: Onderon.[4]

The Emperor brought the Eclipse II to Onderon, where the Solos had relocated their children. While the New Republic engaged the Imperials, a team of Jedi led by Luke Skywalker along with Han Solo, sought out the Emperor. Brand sensed the Emperor's intense darkness in a nearby shuttle. They fought their way to the Emperor's shuttle past his guardsmen and stormtroopers, but did not find him aboard the ship. Instead, they encountered a Dark Side Adept, whom informed them that they had been deceived and that the Emperor has slipped down to the Kira Fortress to find Leia and her child.[4]

The procedure went so fast, the crew of the Millennium Falcon did not have time to detach before the jump, and so went on an involuntary journey towards the Deep Core with the warship. Meanwhile, on the Galaxy Gun, the engineer Umak Leth attempted to aid his Emperor by arming the Gun. As the Galaxy Gun was being prepared, the Eclipse II suddenly came out of hyperspace, ramming the cannon and damaging both vessels.[4]

The Millennium Falcon managed to disconnect from the Star Dreadnought before impact and prepared to enter hyperspace. As the Gun was struck by the Eclipse II, the armed missile was fired by the cannon, in a vain attempt at hitting the ship that was on a collision course. The missile got caught by Byss's gravity well, exploded upon impact and destroyed the planet, taking some of the orbiting fleet along with it, as well as the wrecks of the Galaxy Gun and Eclipse II. The Falcon managed to exit the Beshqek system before being hit by debris from the explosion.[4]

Meanwhile, Palpatine faced Leia and demanded the possession of her youngest child Anakin Solo, stating that he was no longer willing to be gentle to her. She fought back, managing to knock the Emperor off his feet with a powerful Force Push; allowing her children to slip to safety. Enraged, Palpatine stood and unleashed a barrage of Force lightning. Leia fought back but was no match for the Emperor, and was finally knocked unconscious by one of his lightning bolts.[4]

With Leia immobilized, Palpatine now attempted to enter Anakin's body. Before he could complete his plan, Skywalker and two other Jedi—Rayf Ysanna and Empatojayos Brand—arrived. Palpatine, along with two Dark Jedi fatally injured Brand with force Lightning despite his attempts to fight back. However, Palpatine's use of the Force drained his weakened clone body.[4]

The Dark Jedi T'iaz then engaged Ysanna in a lightsaber duel but was killed himself. However, Rayf was then cut down by the Dark Lord himself, whom Rayf had underestimated, even stating that frail old man like Palpatine would be easy to defeat, and that and that he would protect anyone Palpatine tried to harm. Nevertheless, he could not defend himself from the rage and the tremendous power of the Emperor, despite the inferiority of his clone body.[4]

After having killed Rayf, Palpatine noted that it was not the first time he saw a "poor fool" die with the Jedi fire burning in his eyes. Skywalker tried to stop the Emperor from grabbing Anakin. The Emperor ignored Skywalker's warnings and fought back with all his remaining energy against the Jedi Master. Despite the loss of his adepts, he finally managed to grab the boy.[4]

Leia and Han Solo attempted to stop Palpatine's efforts to claim their child. Leia commented that she would only let Palpatine get the baby "over her dead body". Han quickly shot the Emperor in the back, which Palpatine purposely did not block so that he could be free of his physical form and "enter the child as he had promised". Luke knew that this would be the beginning of the end, as they could not fight Palpatine's ghost.[4]

His last clone body destroyed, the Emperor's cackling spirit flew towards young Anakin Solo, but was intercepted by the dying Brand, who threw himself in the way. The Purge survivor shielded the baby with the Light Side of the Force and bound the Emperor's departing life essence to his own, taking it with him as he became one with the Force. Railing and cursing the Skywalkers, Palpatine's spirit was dragged into the depths of Chaos. There he would experience disembodiment in darkness, perpetual madness as if to always live with an open wound, terror without respite.[4]

Darth Sidious, considered by many to be the greatest Dark Lord of the Sith of all time, was finally dead. With his death, the Galactic Empire splintered again into several factions. [3] Because of this, as well as the previous losses sustained by the Imperial Civil War and the Empire Reborn campaign, the Galactic Empire also permanently lost any chance of reconquering the Galaxy.[5]